Link to this post | posted 28 Jun, 2019 15:58

scaruso

Excellent, Question, though. I caught up on the meeting that I had to leave from yesterday and have a question that pertains to this. Perhaps the new version of the virtual machine could include some of these useful tools all put together? The new Starterator from Chris, a standalone Aragorn in case we loose it in the future (or it's down again, or until we can host it somewhere), the new version of the splitstree prep-program, and the newest version of the checker? I'd happily upgrade. Steve

Link to this post | posted 25 Jun, 2019 15:41
scaruso	It won't load for me at all, still. I asked some people to try it at the last SMART meeting, and it didn't load for them either, so there may be something going on. Welkin mentioned she heard there may be a retirement coming up. Steve

Link to this post | posted 19 Jun, 2019 13:32
scaruso	Has anyone been having trouble accessing Aragorn? We have not been able to access it for a couple days now. Steve

Link to this post | posted 24 May, 2019 21:16
scaruso	These are big phages. S.

Link to this post | posted 24 May, 2019 21:12
scaruso	Ah. Thanks. That helps. Steve Edited 24 May, 2019 21:13

Link to this post | posted 24 May, 2019 18:04

scaruso

I am checking a BE1 submission, which have 40+ tRNAs. I noticed, as I go though them that I would not have accepted all of these. I've already found four with acceptor stems of 5 bp, 6 bp, and 8 bp, and a couple with very low scores (10 and 14), but that are present in other BE1 phages. Before I deleted them, I wanted to make sure there was no reason these were in there outside the guidlines. Thanks! Steve Edited 24 May, 2019 18:08

Link to this post | posted 20 May, 2019 21:13

scaruso

We certainly had problems with smears in the past. Most of the time, I have attributed it to user error, and we have switched to adding EDTA and proteinase K to our protocol. It has nearly, but not completely eliminated the issue. I think the few that remain are a mixture mostly of students that are incautious, and a few that are something else. We have phages that simply refuse to give us pretty DNA (the Bacillus phi29-like podos are a reliable example) unless we use phenol chloroform despite very high titers. That's consistent over several years among many students. We have to wonder if there is something interesting going on with their DNA or capsid, or a packaged enzyme that is being denatured by the phenol but not by the standard isolation. Then, this year, we had several, five I think, Streptomyces phages that were not cut at all when tested by every enzyme I could get my hands on (I think I had ten or so). These were enzymes that were consistently cutting other phages' DNA, so we knew they worked. So, not a smear, but modified DNA? Seems like a possibility. Steve

Link to this post | posted 16 May, 2019 18:56
scaruso	OK, so, after further consideration and looking at the second one, I think calling the first gene Lysin A is probably pretty safe. I don't know about calling the second one anything beyond hydrolase. Steve

Link to this post | posted 13 May, 2019 17:03

scaruso

These phages have a second gene identified as hydrolase immediately following two minor tail proteins and immediately before the holin, so it is hard to tell if it is another minor tail protein or a lysin by synteny, so the more generic call has been used in the past. That is - https://toolkit.tuebingen.mpg.de/#/jobs/Esketit_28a and https://toolkit.tuebingen.mpg.de/#/jobs/Esketit_28b Once this is resolved, it's ready, by the way. Steve Edited 13 May, 2019 17:03

Link to this post | posted 12 May, 2019 01:09

scaruso

I am reviewing a BI1 and have a another call that I am planning on deleting, thymidylate kinase. The call has been made based on a blast hit to several other phages, but I can't find any other evidence that it really is thymidylate kinase. If this were one of our phages, I would call it NKF for sure, but wanted to get a second opinion since it is the first one I am reviewing externally. Three members of pham 44619 (https://phagesdb.org/phams/44619/) have the call, the rest don't. The results for the gene are here https://toolkit.tuebingen.mpg.de/#/jobs/Esketit_73a and https://toolkit.tuebingen.mpg.de/#/jobs/Esketit_73b. No hint of a hit other than by blast - https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=DEW588MA015. I think they are questionable hits. But the approved functions list uses Erdmann_94 as the example of the call, which is pham 46029 - https://phagesdb.org/phams/46029/, and has been changed to thymidylate synthase and is mostly filled with ThyX, etc. Upshot is, I think the kinase call wrong. Thoughts? Steve Edited 13 May, 2019 00:01